R 无法加载调用 lapack 函数的库
R cannot load libraries calling lapack functions
我正在尝试安装一些流行的 R 包,但不知何故我的 R 看不到 lapack 安装。或者更确切地说,编译器没有看到它,我猜,因为当它检查 LAPACK_LIBS 时,它说它找到了它。我检查了 sessionInfo() 和 La_version() ,它们都指向 lapack 的安装位置。我该如何解决它?
> install.packages("RcppArmadillo")
Installing package into ‘/homeUPDATES
/marcin/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.10.5.0.0.tar.gz'
Content type 'application/x-gzip' length 1669395 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -L/usr/local/opt/gsl/lib -lgsl -llapack -lgslcblas -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/usr/local/opt/gettext/lib -L/usr/lib/R/lib -lR
installing to /home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘RcppArmadillo’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so':
/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: dgesvx_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/RcppArmadillo’
Warning in install.packages("RcppArmadillo") :
installation of package ‘RcppArmadillo’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpw0yc9E/downloaded_packages’
>
更新 1:
我确保 blas 和 lapack .so 文件具有 755 权限,但没有帮助。
更新 2:
当我尝试从源构建一个需要 lapack 的包时,同样的问题发生了。例如,我尝试使用以下 Makevars
安装 GpGp 包
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
它给出了同样的问题。
在终端中尝试 sudo apt-get update
。是不是说什么东西被锁了?在我看来,其他东西正在使用依赖文件,因此进程被锁定。如果是这种情况,您可以等待该过程完成或重新启动。
你也可以尝试安装forcing no lock:
install.packages("RcppArmadillo",INSTALL_opts = '--no-lock')
您也可以尝试通过遥控器和 github 页面安装,这将为您提供最新的开发版本而不是 cran 版本:
library(remotes)
remotes::install_github("RcppCore/RcppArmadillo")
请安装 openblas-dev 库:
sudo apt -y install libopenblas-dev
未找到符号 dgesvx_
。这些是外部 C 定义,包装到 Fortran 驱动程序。然后搜索符号,你会在这里找到它:
~> grep dgesvx_ /usr/lib/x86_64-linux-gnu/liblapack.so.3
grep: /usr/lib/x86_64-linux-gnu/liblapack.so.3: binary file matches
所以最终我发现问题出在我的 ~/.R/Makevars
文件上。 Dirk 在我最初的问题下的评论让我想知道这些额外的命令是从哪里来的,我在 Makevars
中找到了它们。我不记得我什么时候以及为什么向它添加了一些东西,但是当我恢复到一个空的 Makevars
文件时,一切正常!谢谢德克!
我正在尝试安装一些流行的 R 包,但不知何故我的 R 看不到 lapack 安装。或者更确切地说,编译器没有看到它,我猜,因为当它检查 LAPACK_LIBS 时,它说它找到了它。我检查了 sessionInfo() 和 La_version() ,它们都指向 lapack 的安装位置。我该如何解决它?
> install.packages("RcppArmadillo")
Installing package into ‘/homeUPDATES
/marcin/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.10.5.0.0.tar.gz'
Content type 'application/x-gzip' length 1669395 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -L/usr/local/opt/gsl/lib -lgsl -llapack -lgslcblas -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/usr/local/opt/gettext/lib -L/usr/lib/R/lib -lR
installing to /home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘RcppArmadillo’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so':
/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: dgesvx_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/RcppArmadillo’
Warning in install.packages("RcppArmadillo") :
installation of package ‘RcppArmadillo’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpw0yc9E/downloaded_packages’
>
更新 1:
我确保 blas 和 lapack .so 文件具有 755 权限,但没有帮助。
更新 2:
当我尝试从源构建一个需要 lapack 的包时,同样的问题发生了。例如,我尝试使用以下 Makevars
安装 GpGp 包PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
它给出了同样的问题。
在终端中尝试 sudo apt-get update
。是不是说什么东西被锁了?在我看来,其他东西正在使用依赖文件,因此进程被锁定。如果是这种情况,您可以等待该过程完成或重新启动。
你也可以尝试安装forcing no lock:
install.packages("RcppArmadillo",INSTALL_opts = '--no-lock')
您也可以尝试通过遥控器和 github 页面安装,这将为您提供最新的开发版本而不是 cran 版本:
library(remotes)
remotes::install_github("RcppCore/RcppArmadillo")
请安装 openblas-dev 库:
sudo apt -y install libopenblas-dev
未找到符号 dgesvx_
。这些是外部 C 定义,包装到 Fortran 驱动程序。然后搜索符号,你会在这里找到它:
~> grep dgesvx_ /usr/lib/x86_64-linux-gnu/liblapack.so.3
grep: /usr/lib/x86_64-linux-gnu/liblapack.so.3: binary file matches
所以最终我发现问题出在我的 ~/.R/Makevars
文件上。 Dirk 在我最初的问题下的评论让我想知道这些额外的命令是从哪里来的,我在 Makevars
中找到了它们。我不记得我什么时候以及为什么向它添加了一些东西,但是当我恢复到一个空的 Makevars
文件时,一切正常!谢谢德克!